MYCN overexpression is linked to significant differences in nuclear DNA organization in neuroblastoma

Rangel‐Pozzo, Aline; Kuzyk, Alexandra; Gartner, John G.; Mai, Sabine

doi:10.32392/biomed.63.3

Cited by 5 publications

(10 citation statements)

References 39 publications

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“…This result aligned with our telomere data, which showed more telomere signals and probably more chromosomes. Previous studies have shown that the number of DNA-poor spaces increases in tumor cells [ 12 , 20 , 21 , 22 ], suggesting chromatin remodeling. However, these DNA-free interchromatin areas could be nucleoli, which display the same morphology as DNA-poor spaces and could also be associated with the absence of DNA.…”

Section: Discussionmentioning

confidence: 99%

A Multifocal Pediatric Papillary Thyroid Carcinoma (PTC) Harboring the AGK-BRAF and RET/PTC3 Fusion in a Mutually Exclusive Pattern Reveals Distinct Levels of Genomic Instability and Nuclear Organization

Sisdelli

Cordioli

Vaisman

et al. 2021

Biology

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The spectrum and incidence of gene fusions in papillary thyroid carcinoma (PTC) can differ significantly depending on the age of onset, histological subtype or radiation exposure history. In sporadic pediatric PTC, RET/PTC1-3 and AGK-BRAF fusions are common genetic alterations. The role of RET/PTC as a prognostic marker in pediatric PTC is still under investigation. We recently showed that AGK-BRAF fusion is prevalent in young patients (mean 10 years) and associated with specific and aggressive pathological features such as multifocality and lung metastasis. In this pilot study, we report a unique patient harboring three different foci: the first was positive for AGK-BRAF fusion, the second was positive for just RET/PTC3 fusion and the third was negative for both rearrangements. To investigate whether AGK-BRAF and RET/PTC3 are associated with genomic instability and chromatin modifications, we performed quantitative fluorescence in situ hybridization (Q-FISH) of telomere repeats followed by 3D imaging analysis and 3D super-resolution Structured Illumination Microscopy (3D-SIM) to analyze the DNA structure from the foci. We demonstrated in this preliminary study that AGK-BRAF is likely associated with higher levels of telomere-related genomic instability and chromatin remodeling in comparison with RET/PTC3 foci. Our results suggest a progressive disruption in chromatin structure in AGK-BRAF-positive cells, which might explain a more aggressive disease outcome in patients harboring this rearrangement.

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Section: Discussionmentioning

confidence: 99%

A Multifocal Pediatric Papillary Thyroid Carcinoma (PTC) Harboring the AGK-BRAF and RET/PTC3 Fusion in a Mutually Exclusive Pattern Reveals Distinct Levels of Genomic Instability and Nuclear Organization

Sisdelli

Cordioli

Vaisman

et al. 2021

Biology

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“…Notably, the CRISPR p53 deleted cells show more DNA-free/poor spaces than their normal counterparts (indicated with circles), a characteristic of tumor cells [58][59][60]. From the 3D-SIM images, the different length-scales of DNA organization can be interpreted as granules with different diameters, and the cumulative size distribution of DNA structures can be represented as a curve showing the distribution of different granule sizes in that particular cell [58][59][60]. Histograms for the structure of DNA and structure of DNA-poor spaces for MCF-7 (wt and CRISPR-p53) and normal breast cell lines are shown in Figure 1B.…”

Section: Analysis Of Dna Sstructure Reveals Differences In Dna Structmentioning

confidence: 99%

“…3D-SIM can offer the ability to capture resolutions up to 100 nm resolution in the xand yaxes and 200-250 nm in the z-axis, which can reveal structural information much closer to the scale of higher order DNA structures within the nucleus [56,57]. This technique has previously been used to quantify broad scale changes in DNA ultrastructure that occur after malignant transformation in cancers [58][59][60]. 3D-SIM technology can be used to capture the size and intensity of fluorescent DNA signals in three dimensions in nuclei stained with DAPI (4 ,6 diamidino-2-phenylindole), revealing the size distribution of DNA structures and DNA-poor spaces in super-resolution imaging.…”

Section: Introductionmentioning

confidence: 99%

“…3D-SIM technology can be used to capture the size and intensity of fluorescent DNA signals in three dimensions in nuclei stained with DAPI (4 ,6 diamidino-2-phenylindole), revealing the size distribution of DNA structures and DNA-poor spaces in super-resolution imaging. The granulometry program calculates the cumulative distribution of micron and submicron DNA "granules" within the cell nucleus, as resolved by 3D-SIM technology [58][59][60]. Previous analysis has shown that coarser chromatin texture is associated with dysregulated nuclear architecture in cancer when compared to non-transformed cells [58][59][60].…”

Section: Introductionmentioning

confidence: 99%

“…The granulometry program calculates the cumulative distribution of micron and submicron DNA "granules" within the cell nucleus, as resolved by 3D-SIM technology [58][59][60]. Previous analysis has shown that coarser chromatin texture is associated with dysregulated nuclear architecture in cancer when compared to non-transformed cells [58][59][60]. The current work assesses the effect of p53 knockout and pharmacological reactivation of p53 on DNA structure in a quantitative manner.…”

Section: Introductionmentioning

confidence: 99%

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p53 CRISPR Deletion Affects DNA Structure and Nuclear Architecture

Rangel‐Pozzo

Booth

et al. 2020

JCM

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The TP53 gene is a key tumor suppressor. Although the tumor suppressor p53 was one of the first to be characterized as a transcription factor, with its main function potentiated by its interaction with DNA, there are still many unresolved questions about its mechanism of action. Here, we demonstrate a novel role for p53 in the maintenance of nuclear architecture of cells. Using three-dimensional (3D) imaging and spectral karyotyping, as well as super resolution microscopy of DNA structure, we observe significant differences in 3D telomere signatures, DNA structure and DNA-poor spaces as well gains or losses of chromosomes, between normal and tumor cells with CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-deleted or wild-type TP53. Additionally, treatment with Nutlin-3 results in differences in nuclear architecture of telomeres in wild-type but not in p53 knockout MCF-7 (Michigan Cancer Foundation-7) cells. Nutlin-3 binds to the p53-binding pocket of mouse double minute 2 (MDM2) and blocks the p53-MDM2 interaction. Moreover, we demonstrate that another p53 stabilizing small molecule, RITA (reactivation of p53 and induction of tumor cell apoptosis), also induces changes in 3D DNA structure, apparently in a p53 independent manner. These results implicate p53 activity in regulating nuclear organization and, additionally, highlight the divergent effects of the p53 targeting compounds Nutlin-3 and RITA.

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Three‐dimensional nuclear architecture distinguishes thyroid cancer histotypes

Rangel‐Pozzo

Santos

Dettori

et al. 2023

Intl Journal of Cancer

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Molecular markers can serve as diagnostic tools to support pathological analysis in thyroid neoplasms. However, because the same markers can be observed in some benign thyroid lesions, additional approaches are necessary to differentiate thyroid tumor subtypes, prevent overtreatment and tailor specific clinical management. This applies particularly to the recently described variant of thyroid cancer referred to as noninvasive follicular thyroid neoplasm with papillary‐like nuclear features (NIFTP). This variant has an estimated prevalence of 4.4% to 9.1% of all papillary thyroid carcinomas worldwide. We studied 60 thyroid lesions: 20 classical papillary thyroid carcinoma (CPTC), 20 follicular variant of PTC (FVPTC) and 20 NIFTP. We examined morphological and molecular features to identify parameters that can differentiate NIFTP from the other PTC subtypes. When blindly investigating the nuclear architecture of thyroid neoplasms, we observed that NIFTP has significantly longer telomeres than CPTC and FVPTC. Super‐resolved 3D‐structured illumination microscopy demonstrated that NIFTP is heterogeneous and that its nuclei contain more densely packed DNA and smaller interchromatin spaces than CPTC and FVPTC, a pattern that resembles normal thyroid tissue. These data are consistent with the observed indolent biological behavior and favorable prognosis associated with NIFTP, which lacks BRAFV600E mutations. Of note, next‐generation thyroid oncopanel sequencing was unable to distinguish the thyroid cancer histotypes in our study cohort. In summary, our data suggest that 3D nuclear architecture can be a powerful analytical tool to diagnose and guide clinical management of NIFTP.

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MYCN overexpression is linked to significant differences in nuclear DNA organization in neuroblastoma

Abstract: Rangel-Pozzo et al. (2019) MYCN overexpression is linked to significant differences in nuclear DNA organization in neuroblastoma. SPG BioMed 1(2).

Cited by 5 publications

References 39 publications

A Multifocal Pediatric Papillary Thyroid Carcinoma (PTC) Harboring the AGK-BRAF and RET/PTC3 Fusion in a Mutually Exclusive Pattern Reveals Distinct Levels of Genomic Instability and Nuclear Organization

A Multifocal Pediatric Papillary Thyroid Carcinoma (PTC) Harboring the AGK-BRAF and RET/PTC3 Fusion in a Mutually Exclusive Pattern Reveals Distinct Levels of Genomic Instability and Nuclear Organization

p53 CRISPR Deletion Affects DNA Structure and Nuclear Architecture

Three‐dimensional nuclear architecture distinguishes thyroid cancer histotypes

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